From 2b13f775c9f4c7f666a5d69191d2fb30bcb32341 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 23 Feb 2007 15:09:23 +0000
Subject: [PATCH] Allow the Xref parsers to read gzip compressed files through
a zcat pipe. Use the command line switch -compressed with xref_parser.pl to
do this. The default behaviour (without the -compressed switch) is still to
uncompress gzipped files.
---
.../XrefParser/AedesGenBankParser.pm | 26 ++--
.../xref_mapping/XrefParser/AgilentParser.pm | 27 ++---
.../XrefParser/AnophelesSymbolParser.pm | 26 ++--
.../xref_mapping/XrefParser/BaseParser.pm | 113 +++++++++++++-----
.../xref_mapping/XrefParser/CCDSParser.pm | 28 ++---
.../xref_mapping/XrefParser/CeleraParser.pm | 22 +---
.../XrefParser/CeleraProteinParser.pm | 21 +---
.../XrefParser/CeleraTranscriptParser.pm | 21 +---
.../xref_mapping/XrefParser/CodelinkParser.pm | 24 ++--
.../xref_mapping/XrefParser/DatabaseParser.pm | 12 +-
.../XrefParser/EntrezGeneParser.pm | 31 ++---
.../xref_mapping/XrefParser/FastaParser.pm | 14 +--
.../XrefParser/Flybase_dmel_GFFv3_Parser.pm | 23 ++--
.../xref_mapping/XrefParser/GOParser.pm | 27 ++---
.../xref_mapping/XrefParser/HUGOParser.pm | 25 ++--
.../XrefParser/HUGO_CCDSParser.pm | 24 ++--
.../XrefParser/HUGO_ENSGParser.pm | 26 ++--
.../xref_mapping/XrefParser/IPIParser.pm | 26 ++--
.../xref_mapping/XrefParser/IlluminaParser.pm | 23 +---
.../xref_mapping/XrefParser/InterproParser.pm | 31 ++---
.../xref_mapping/XrefParser/JGI_Parser.pm | 31 ++---
.../XrefParser/JGI_ProteinParser.pm | 13 +-
.../xref_mapping/XrefParser/MGDParser.pm | 44 +++----
.../xref_mapping/XrefParser/MIMParser.pm | 36 +++---
.../xref_mapping/XrefParser/OTTTParser.pm | 26 ++--
.../xref_mapping/XrefParser/RGDParser.pm | 27 ++---
.../XrefParser/RefSeqGPFFParser.pm | 32 ++---
.../xref_mapping/XrefParser/RefSeqParser.pm | 48 ++++----
.../XrefParser/RefSeq_CCDSParser.pm | 30 ++---
.../xref_mapping/XrefParser/SGDParser.pm | 29 ++---
.../xref_mapping/XrefParser/SegmentParser.pm | 26 ++--
.../xref_mapping/XrefParser/UniGeneParser.pm | 49 ++++----
.../xref_mapping/XrefParser/UniProtParser.pm | 38 ++----
.../XrefParser/UniProtVarSplicParser.pm | 29 ++---
.../XrefParser/WilsonAffyParser.pm | 35 +++---
.../xref_mapping/XrefParser/WormPepParser.pm | 25 ++--
.../WormbaseDatabaseStableIDParser.pm | 13 +-
.../XrefParser/XenopusJamboreeParser.pm | 26 ++--
.../xref_mapping/XrefParser/ZFINParser.pm | 46 ++++---
.../xref_mapping/XrefParser/ncRNAParser.pm | 26 ++--
misc-scripts/xref_mapping/xref_parser.pl | 62 ++++++----
41 files changed, 508 insertions(+), 753 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm b/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
index 5769b8da38..7fb3838057 100644
--- a/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm
@@ -3,10 +3,7 @@ package XrefParser::AedesGenBankParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
#Aedes GenBank protein - because not yet in UniProt
#>EAT48991.1
@@ -25,11 +22,13 @@ sub run {
local $/ = "\n>";
- if(!open(FILE,"<".$file)){
- print "Could not open $file\n";
- return 1;
+ my $file_io = $self->get_filehandle($file);
+ if ( !defined $file_io ) {
+ print "Could not open $file\n";
+ return 1;
}
- while (<FILE>) {
+
+ while ( $_ = $file_io->getline() ) {
my $xref;
@@ -73,7 +72,7 @@ sub run {
}
- close (FILE);
+ $file_io->close();
print scalar(@xrefs) . " AedesGenBank xrefs succesfully parsed\n";
@@ -83,13 +82,4 @@ sub run {
return 0;
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::AedesGenBankParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm b/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm
index 0817341726..a9a37f555c 100644
--- a/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AgilentParser.pm
@@ -3,10 +3,7 @@ package XrefParser::AgilentParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# OParser for FASTA-format probe mappings from Agilent
# >A_23_P253586
@@ -22,12 +19,15 @@ sub run {
# local $/ = "\n>";
- if(!open(AG,"<".$file)){
- print "Could not open $file\n";
- return 1;
+ my $ag_io = $self->get_filehandle($file);
+
+ if ( !defined $ag_io ) {
+ print "Could not open $file\n";
+ return 1;
}
+
my $probe;
- while (<AG>) {
+ while ( $_ = $ag_io->getline() ) {
chomp;
@@ -57,7 +57,7 @@ sub run {
}
}
- close(AG);
+ $ag_io->close();
print scalar(@xrefs) . " Agilent xrefs succesfully parsed\n";
@@ -67,13 +67,4 @@ sub run {
return 0;
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::AgilentParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm b/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
index eaf5a838e7..641b724dfb 100644
--- a/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm
@@ -3,10 +3,7 @@ package XrefParser::AnophelesSymbolParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# AnophelesSymbol database dump for anopheles - FASTA format
#
@@ -25,12 +22,14 @@ sub run {
local $/ = "\n>";
- if(!open(FILE,"<".$file)){
- print "Could not open $file\n";
- return 1;
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
+ print "Could not open $file\n";
+ return 1;
}
- while (<FILE>) {
+ while ( $_ = $file_io->getline() ) {
my $xref;
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
@@ -55,7 +54,7 @@ sub run {
}
- close (FILE);
+ $file_io->close();
print scalar(@xrefs) . " AnophelesSymbol xrefs succesfully parsed\n";
@@ -65,13 +64,4 @@ sub run {
return 0;
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::AnophelesSymbolParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
index 9b368624af..ebcaf7246b 100644
--- a/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/BaseParser.pm
@@ -27,16 +27,27 @@ my %dependent_sources;
my %taxonomy2species_id;
my %name2species_id;
-my ($host, $port, $dbname, $user, $pass, $create, $release, $cleanup, $deletedownloaded);
-my ($skipdownload,$drop_db,$checkdownload, $dl_path) ;
+my (
+ $host, $port, $dbname,
+ $user, $pass, $create,
+ $release, $cleanup, $deletedownloaded,
+ $skipdownload, $drop_db, $checkdownload,
+ $dl_path, $compressed
+);
# --------------------------------------------------------------------------------
# Get info about files to be parsed from the database
-sub run {
-
- ($host, $port, $dbname, $user, $pass, my $speciesr, my $sourcesr, $skipdownload, $checkdownload,
- $create, $release, $cleanup, $drop_db, $deletedownloaded, $dl_path, my $notsourcesr) = @_;
+sub run
+{
+ (
+ $host, $port, $dbname,
+ $user, $pass, my $speciesr,
+ my $sourcesr, $skipdownload, $checkdownload,
+ $create, $release, $cleanup,
+ $drop_db, $deletedownloaded, $dl_path,
+ my $notsourcesr, $compressed
+ ) = @_;
$base_dir = $dl_path if $dl_path;
@@ -195,8 +206,8 @@ sub run {
if ($checkdownload) {
my $check_file = $dir . '/' . $file;
- $check_file =~ s/\.gz$//;
- $check_file =~ s/\.Z$//;
+
+ if ( !$compressed ) { $check_file =~ s/\.(gz|Z)$// }
print "Checking for file '$check_file'\n";
@@ -206,8 +217,7 @@ sub run {
$skipdownload = 1;
- $file =~ s/\.gz$//;
- $file =~ s/\.Z$//;
+ if ( !$compressed ) { $file =~ s/\.(gz|Z)$// }
} else {
print "File '$check_file' does not exist.\n"
. "Scheduling '$dir/$file' for download...\n";
@@ -265,22 +275,27 @@ sub run {
croak("Could not get $type file $file tried 5 times but failed");
}
- # if the file is compressed, the FTP server may or may not have automatically uncompressed it
- # TODO - read .gz file directly? open (FILE, "zcat $file|") or Compress::Zlib
- if ($file =~ /(.*)\.gz$/ or $file =~ /(.*)\.Z$/) {
- print "Uncompressing $dir/$file\n";
- system("gunzip -f $dir/$file");
- $file = $1;
- }
- if ($file =~ /(.*)\.zip$/) {
- print "Unzipping $dir/$file\n";
- system("unzip -o -q -d $dir $dir/$file");
- }
+ # If the file is compressed, the FTP server may or may not have
+ # automatically uncompressed it (it shouldn't have, is this an
+ # historical artifact? (ak)).
+
+ if ( !$compressed && ( $file =~ /\.(gz|Z)$/ ) ) {
+ print "Uncompressing '$dir/$file' using 'gunzip'\n";
+ system( "gunzip", "-f", $dir . '/' . $file );
+ }
+ if ( $file =~ /(.*)\.zip$/ ) {
+ print "Uncompressing '$dir/$file' using 'unzip'\n";
+ system( "unzip", "-o", "-q", "-d", $dir,
+ $dir . '/' . $file );
+ }
}
- $file =~s/\.gz$//; # if skipdownload set this will not have been done yet.
- $file=~s/\.Z$//; # if it has no harm done
+ if ( !$compressed ) {
+ $file =~ s/\.(gz|Z)$//; # If skipdownload set this will
+ # not have been done yet.
+ # If it has, no harm done
+ }
if ($file_from_archive) {
push @new_file, $file_from_archive;
@@ -361,13 +376,57 @@ sub run {
# --------------------------------------------------------------------------------
-sub new {
+# Given a file name, returns a IO::Handle object. If the file is
+# gzipped, the handle will be to an unseekable stream coming out of a
+# zcat pipe. If the given file name doesn't correspond to an existing
+# file, the routine will try to add '.gz' to the file name or to remove
+# any .'Z' or '.gz' and try again. Returns undef on failure and will
+# write a warning to stderr.
+
+sub get_filehandle
+{
+ my ($self, $file_name) = @_;
+
+ my $io;
+
+ my $alt_file_name = $file_name;
+ $alt_file_name =~ s/\.(gz|Z)$//;
- my $self = {};
- bless $self, "BaseParser";
+ if ( $alt_file_name eq $file_name ) {
+ $alt_file_name .= '.gz';
+ }
+
+ if ( !-f $file_name ) {
+ carp( "File '$file_name' does not exist, "
+ . "will try '$alt_file_name'" );
+ $file_name = $alt_file_name;
+ }
+
+ if ( $file_name =~ /\.(gz|Z)$/ ) {
+ # Read from zcat pipe
+ $io = IO::File->new("zcat $file_name |")
+ or carp("Can not open file '$file_name' with 'zcat'");
+ } else {
+ # Read file normally
+ $io = IO::File->new($file_name)
+ or carp("Can not open file '$file_name'");
+ }
+
+ if ( !defined $io ) { return undef }
- return $self;
+ print "Reading from '$file_name'...\n";
+
+ return $io;
+}
+
+# --------------------------------------------------------------------------------
+
+sub new
+{
+ my ($proto) = @_;
+ my $class = ref $proto || $proto;
+ return bless {}, $class;
}
# --------------------------------------------------------------------------------
diff --git a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
index 877a5995a3..e5fdc637b6 100644
--- a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
@@ -4,10 +4,7 @@ use strict;
use DBI;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Parse file of CCDS records and assign direct xrefs
# All assumed to be linked to transcripts
@@ -18,17 +15,19 @@ sub run {
my ($self, $file, $source_id, $species_id) = @_;
- if(!open(CCDS,"<".$file)){
- print "Could not open $file\n";
- return 1;
+ my $ccds_io = $self->get_filehandle($file);
+
+ if ( !defined $ccds_io ) {
+ print "Could not open $file\n";
+ return 1;
}
+
my $line_count = 0;
my $xref_count = 0;
my $xref_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND version=? AND source_id=$source_id AND species_id=$species_id");
- while (<CCDS>) {
-
+ while ( $_ = $ccds_io->getline() ) {
my ($stable_id, $ccds) = split;
my ($acc, $version) = split (/\./, $ccds);
@@ -48,17 +47,8 @@ sub run {
print "Parsed $line_count CCDS identifiers from $file, added $xref_count xrefs and $line_count direct_xrefs\n";
- close(CCDS);
+ $ccds_io->close();
return 0;
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::CCDSParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm b/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
index ab51ee815d..0d65429397 100644
--- a/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CeleraParser.pm
@@ -3,10 +3,7 @@ package XrefParser::CeleraParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Celera database dump for anopheles - FASTA format
#
@@ -27,12 +24,14 @@ sub run {
local $/ = "\n>";
- if(!open(FILE,"<".$file)){
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
print "Could not open $file\n";
return 1;
}
- while (<FILE>) {
+ while ( $_ = $file_io->getline() ) {
next if (/^File:/); # skip header
my $xref;
@@ -69,7 +68,7 @@ sub run {
}
- close (FILE);
+ $file_io->close();
print scalar(@xrefs) . " Celera xrefs succesfully parsed\n";
@@ -79,13 +78,4 @@ sub run {
return 0;
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::CeleraParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm b/misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm
index 1325537fb7..a51cc21403 100644
--- a/misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm
@@ -2,26 +2,13 @@ package XrefParser::CeleraProteinParser;
use strict;
-use XrefParser::CeleraParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::CeleraParser);
+use base qw( XrefParser::CeleraParser );
# See CeleraParser for details
-sub get_sequence_type() {
-
- return 'peptide';
-
-}
-
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::CeleraProteinParser";
- return $self;
-
+sub get_sequence_type()
+{
+ return 'peptide';
}
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm b/misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm
index 99a2e8de6e..fb08e9f140 100644
--- a/misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm
@@ -2,26 +2,13 @@ package XrefParser::CeleraTranscriptParser;
use strict;
-use XrefParser::CeleraParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::CeleraParser);
+use base qw( XrefParser::CeleraParser );
# See CeleraParser for details
-sub get_sequence_type() {
-
- return 'dna';
-
-}
-
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::CeleraTranscriptParser";
- return $self;
-
+sub get_sequence_type()
+{
+ return 'dna';
}
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm b/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm
index 433ce2e043..061ad01da6 100644
--- a/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm
@@ -3,10 +3,7 @@ package XrefParser::CodelinkParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Parser for Codelink probes
@@ -23,13 +20,13 @@ sub run {
local $/ = "\n>";
- if(!open(CODELINK,"<".$file)){
+ my $codelink_io = $self->get_filehandle($file);
+ if ( !defined $codelink_io ) {
print "ERROR: Could not open $file\n";
- return 1; # 1 = error
+ return 1; # 1 = error
}
- while (<CODELINK>) {
-
+ while ( $_ = $codelink_io->getline() ) {
my $xref;
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
@@ -53,6 +50,8 @@ sub run {
}
+ $codelink_io->close();
+
print scalar(@xrefs) . " Codelink xrefs succesfully parsed\n";
XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
@@ -61,13 +60,4 @@ sub run {
return 0; #successful
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::CodelinkParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/DatabaseParser.pm b/misc-scripts/xref_mapping/XrefParser/DatabaseParser.pm
index a63494a011..ac72f18c90 100644
--- a/misc-scripts/xref_mapping/XrefParser/DatabaseParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/DatabaseParser.pm
@@ -3,10 +3,8 @@ package XrefParser::DatabaseParser;
use strict;
use DBI;
-use XrefParser::BaseParser;
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Base class for parsers that parse from databases rather than files
@@ -58,13 +56,5 @@ sub db {
}
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::DatabaseParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm b/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
index c17780f382..750e46e1d1 100644
--- a/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm
@@ -4,11 +4,7 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
-
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -41,14 +37,15 @@ sub run {
my $species_tax_id = $self->get_taxonomy_from_species_id($species_id);
- if(!open(EG,"<".$file)){
- print "ERROR: Could not open $file\n";
- return 1; # 1 is an error
- }
+ my $eg_io = $self->get_filehandle($file);
+ if ( !defined $eg_io ) {
+ print "ERROR: Could not open $file\n";
+ return 1; # 1 is an error
+ }
- my $head = <EG>; # first record are the headers
+ my $head = $eg_io->getline(); # first record are the headers
chomp $head;
my (@arr) = split(/\s+/,$head);
# process this to the correct indexes to use. (incase they change);
@@ -92,7 +89,7 @@ sub run {
}
my $xref_count = 0;
my $syn_count = 0;
- while (<EG>) {
+ while ( $_ = $eg_io->getline() ) {
chomp;
my (@arr) = split(/\t/,$_);
if($arr[$gene_tax_id_index] != $species_tax_id){
@@ -110,18 +107,12 @@ sub run {
$syn_count++;
}
}
+
+ $eg_io->close();
+
print $xref_count." EntrezGene Xrefs added with $syn_count synonyms\n";
return 0; #successful
}
-
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::EntrezGeneParser";
- return $self;
-
-}
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/FastaParser.pm b/misc-scripts/xref_mapping/XrefParser/FastaParser.pm
index 44da5797de..ebde3171f0 100644
--- a/misc-scripts/xref_mapping/XrefParser/FastaParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/FastaParser.pm
@@ -4,10 +4,7 @@ use strict;
use Bio::SeqIO;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Fasta file format, e.g.
# >foo peptide sequence for the foo gene
@@ -55,13 +52,4 @@ sub run {
return 0; #successful
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::FastaParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm b/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
index 653589e35a..31db32db96 100644
--- a/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm
@@ -10,14 +10,12 @@
package XrefParser::Flybase_dmel_GFFv3_Parser;
use strict;
+
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-use vars qw(@ISA);
use Bio::EnsEMBL::Utils::Exception;
-
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
my %cache_source =();
@@ -40,9 +38,8 @@ if (!defined(caller())) {
# --------------------------------------------------------------------------------
sub new {
- my ($class,@args) = @_;
- my $self={};
- bless $self,$class;
+ my $proto = shift;
+ my $self = $proto->SUPER::new(@_);
$self->external_source_db_name('flybase_gff');
@@ -165,11 +162,15 @@ sub create_xrefs {
my ($self, $flybase_source_id, $file) = @_;
print STDERR "starting to parse $file...." ;
- if(!open(GFF, $file)){
+
+ my $gff_io = $self->get_filehandle($file);
+
+ if ( !defined $gff_io ) {
print "ERROR: Can't open the GFF file $file\n";
return 0;
}
- while (<GFF>) {
+
+ while ( $_ = $gff_io->getline() ) {
chomp;
my @col = split /\s+/;
if($col[3]){
@@ -202,7 +203,9 @@ sub create_xrefs {
}
}
- close (GFF);
+
+ $gff_io->close();
+
return 1;
}
diff --git a/misc-scripts/xref_mapping/XrefParser/GOParser.pm b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
index 00869d3d6f..eac9d917f3 100644
--- a/misc-scripts/xref_mapping/XrefParser/GOParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/GOParser.pm
@@ -6,12 +6,7 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
-
-
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -63,13 +58,16 @@ sub run {
my $count = 0;
- if(!open(GO,"<".$file)){
+ my $go_io = $self->get_filehandle($file);
+
+ if ( !defined $go_io ) {
print "ERROR: Could not open $file\n";
- return 1; # 1 error
+ return 1; # 1 error
}
+
my $taxon_line = "taxon:".$species_id;
my $miss =0;
- while (<GO>) {
+ while ( $_ = $go_io->getline() ) {
if(/$taxon_line/){
chomp;
my @array = split (/\t/,$_);
@@ -168,16 +166,11 @@ sub run {
}
}
}
+
+ $go_io->close();
+
print "\t$count GO dependent xrefs added $refseq_miss refseq not found and $swiss_miss Swissprot not found \n";
return 0;
}
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::GOParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm b/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm
index 1ff87fa540..c207105f6f 100644
--- a/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HUGOParser.pm
@@ -3,10 +3,8 @@ package XrefParser::HUGOParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
+use base qw( XrefParser::BaseParser );
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
my $xref_sth ;
my $dep_sth;
my $syn_sth;
@@ -67,18 +65,20 @@ sub run {
my $entrezgene_count = 0;
my $mismatch = 0;
- if(!open (HUGO, "<$file")){
- print "ERROR: Can't open HUGO file $file\n";
+ my $hugo_io = $self->get_filehandle($file);
+
+ if ( !defined $hugo_io ) {
+ print "ERROR: Can't open HUGO file $file\n";
return 1;
}
- <HUGO>;
+ $_ = $hugo_io->getline();
#23 ABAT 4-aminobutyrate aminotransferase P80404
#29 ABCA1 ATP-binding cassette, sub-family A (ABC1), member 1 ABC1, HDLDT1 O95477
#40 ABCB1 ATP-binding cassette, sub-family B (MDR/TAP), member 1 PGY1, MDR1, CLCS P-gp, CD243, GP170, ABC20 P08183 NM_000927
- while (<HUGO>) {
+ while ( $_ = $hugo_io->getline() ) {
chomp;
@@ -168,7 +168,7 @@ sub run {
} # while HUGO
- close (HUGO);
+ $hugo_io->getline();
print "Loaded a total of " . ($swiss_count + $refseq_count + $entrezgene_count) . " HUGO xrefs, $refseq_count from RefSeq curated mappings and $swiss_count from Uniprot (mapped) and $entrezgene_count from EntrezGene mappings\n";
@@ -182,15 +182,6 @@ sub rename_url_file{
return "hugo.txt";
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::HUGOParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/HUGO_CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/HUGO_CCDSParser.pm
index 394cf49af5..ca172bf50f 100644
--- a/misc-scripts/xref_mapping/XrefParser/HUGO_CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HUGO_CCDSParser.pm
@@ -4,10 +4,7 @@ use strict;
use DBI;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Parse file of HGNC records and assign direct xrefs
# All assumed to be linked to genes
@@ -16,7 +13,9 @@ sub run {
my ($self, $file, $source_id, $species_id) = @_;
- if(!open(HUGO,"<".$file)){
+ my $hugo_io = $self->get_filehandle($file);
+
+ if ( !defined $hugo_io ) {
print "Could not open $file\n";
return 1;
}
@@ -68,7 +67,8 @@ sub run {
my %seen;
my $ignore_count = 0;
my $ignore_examples ="";
- while(<HUGO>){
+
+ while( $_ = $hugo_io->getline() ) {
chomp;
my ($ccds,$hgnc) = split;
@@ -96,17 +96,9 @@ sub run {
print $ignore_count." ignoreed due to numbers no identifiers being no longer valid :- $ignore_examples\n";
}
- close(HUGO);
- return 0;
+ $hugo_io->close();
-}
-
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::HUGO_CCDSParser";
- return $self;
+ return 0;
}
diff --git a/misc-scripts/xref_mapping/XrefParser/HUGO_ENSGParser.pm b/misc-scripts/xref_mapping/XrefParser/HUGO_ENSGParser.pm
index af972d8015..664904ff7b 100644
--- a/misc-scripts/xref_mapping/XrefParser/HUGO_ENSGParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/HUGO_ENSGParser.pm
@@ -4,10 +4,7 @@ use strict;
use DBI;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Parse file of HGNC records and assign direct xrefs
# All assumed to be linked to genes
@@ -16,15 +13,16 @@ sub run {
my ($self, $file, $source_id, $species_id) = @_;
- if(!open(HUGO,"<".$file)){
+ my $hugo_io = $self->get_filehandle($file);
+
+ if ( !defined $hugo_io ) {
print "Could not open $file\n";
return 1;
}
+
my $line_count = 0;
my $xref_count = 0;
-
-
# becouse the direct mapping have no descriptions etc
# we have to steal these fromt he previous HUGO parser.
# This is why the order states this is after the other one.
@@ -51,7 +49,8 @@ sub run {
my $ignore_count = 0;
my $ignore_examples ="";
my %acc;
- while (<HUGO>) {
+
+ while ( $_ = $hugo_io->getline() ) {
my ($hgnc, $stable_id) = split;
@@ -79,17 +78,10 @@ sub run {
if($ignore_count){
print $ignore_count." ignoreed due to numbers no identifiers being no longer valid :- $ignore_examples\n";
}
- close(HUGO);
- return 0;
-}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::HUGO_ENSGParser";
- return $self;
+ $hugo_io->close();
+ return 0;
}
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/IPIParser.pm b/misc-scripts/xref_mapping/XrefParser/IPIParser.pm
index e37d31b080..0f62360f24 100644
--- a/misc-scripts/xref_mapping/XrefParser/IPIParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IPIParser.pm
@@ -3,10 +3,7 @@ package XrefParser::IPIParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# IPI file format: fasta, e.g.
# >IPI:IPI00000005.1|SWISS-PROT:P01111|TREMBL:Q15104|REFSEQ_NP:NP_002515|ENSEMBL:ENSP00000261444 Tax_Id=9606 Transforming protein N-Ras
@@ -22,14 +19,16 @@ sub run {
local $/ = "\n>";
- if(!open(IPI,"<".$file)){
+ my $ipi_io = $self->get_filehandle($file);
+
+ if ( !defined $ipi_io ) {
print "ERROR: Could not open $file\n";
- return 1; # 1 = error
+ return 1; # 1 = error
}
- my $species_tax_id = $self->get_taxonomy_from_species_id($species_id);
- while (<IPI>) {
+ my $species_tax_id = $self->get_taxonomy_from_species_id($species_id);
+ while ( $_ = $ipi_io->getline() ) {
my $xref;
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
@@ -64,6 +63,8 @@ sub run {
}
+ $ipi_io->close();
+
print scalar(@xrefs) . " IPI xrefs succesfully parsed\n";
XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
@@ -72,13 +73,4 @@ sub run {
return 0; #successful
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::IPIParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm b/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm
index 10be9f5d07..d959b579b0 100644
--- a/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm
@@ -2,10 +2,7 @@ package XrefParser::IlluminaParser;
use strict;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Parser for Illumina V2 xrefs - V1 are done by the vanilla FastaParser
@@ -21,13 +18,14 @@ sub run {
my @xrefs;
- if(!open(FILE,"<".$file)){
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
print "Could not open $file\n";
return 1;
}
- while (<FILE>) {
-
+ while ( $_ = $file_io->getline() ) {
chomp;
my $xref;
@@ -63,7 +61,7 @@ sub run {
}
- close(FILE);
+ $file_io->close();
print scalar(@xrefs) . " Illumina V2 xrefs succesfully parsed\n";
@@ -73,13 +71,4 @@ sub run {
return 0;
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::IlluminaParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/InterproParser.pm b/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
index 31e7706bf6..defaf5fd35 100644
--- a/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/InterproParser.pm
@@ -4,11 +4,8 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
+use base qw( XrefParser::BaseParser );
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
-
my $xref_sth ;
my $dep_sth;
@@ -57,15 +54,18 @@ sub run {
my $dir = dirname($file);
-
+
my %short_name;
my %description;
my %pfam;
-
- if(!open (XML, $dir."/interpro.xml")){
+
+ my $xml_io = $self->get_filehandle( $dir . "/interpro.xml" );
+
+ if ( !defined $xml_io ) {
print "ERROR: Can't open hugo interpro file $dir/interpro.xml\n";
- return 1; # 1= error
+ return 1; # 1= error
}
+
#<interpro id="IPR001023" type="Family" short_name="Hsp70" protein_count="1556">
# <name>Heat shock protein Hsp70</name>
# <db_xref protein_count="18" db="PFAM" dbkey="PF01278" name="Omptin" />
@@ -77,8 +77,8 @@ sub run {
my $last = "";
my $i =0;
- while (<XML>) {
+ while ( $_ = $xml_io->getline() ) {
my $interpro;
my $short_name;
my $name;
@@ -109,7 +109,8 @@ sub run {
}
}
- close (LONG);
+ $xml_io->close();
+
for my $db ( keys %count ) {
print "\t".$count{$db}." $db loaded.\n";
}
@@ -126,14 +127,4 @@ sub get_xref{
return 0;
}
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::InterproParser";
- return $self;
-
-}
-
1;
-
-
diff --git a/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm b/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm
index 58377e3011..4cb15cd0a2 100644
--- a/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm
@@ -3,10 +3,7 @@ package XrefParser::JGI_Parser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# JGI protein file with gene predictons - FASTA FORMAT
#
@@ -50,11 +47,14 @@ sub run {
local $/ = "\n>";
- if(!open(FILE,"<".$file)){
- print "ERROR: Could not open $file\n";
- return 1; # 1 is an error
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
+ print "ERROR: Could not open $file\n";
+ return 1; # 1 is an error
}
- while (<FILE>) {
+
+ while ( $_ = $file_io->getline() ) {
next if (/^File:/); # skip header
@@ -122,7 +122,7 @@ sub run {
}
- close (FILE);
+ $file_io->close();
print scalar(@xrefs) . " JGI_ xrefs succesfully parsed\n";
@@ -133,11 +133,14 @@ sub run {
}
-sub new {
- my $self = {};
- bless $self, "XrefParser::JGI_Parser";
- print "\n\nh ave new jp\n" ;
- return $self;
+sub new
+{
+ my $proto = shift;
+ my $self = $proto->SUPER::new(@_);
+
+ print "\n\nhave new jp\n";
+
+ return $self;
}
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm b/misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm
index 218e8fe9dc..90afb658b7 100644
--- a/misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm
@@ -3,21 +3,12 @@ package XrefParser::JGI_ProteinParser;
use strict;
-use XrefParser::JGI_Parser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::JGI_Parser);
+use base qw( XrefParser::JGI_Parser );
# See JGI_Parser for details
+
sub get_sequence_type() {
return 'peptide';
}
-
-sub new {
- my $self = {};
- bless $self, "XrefParser::JGI_ProteinParser";
- return $self;
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/MGDParser.pm b/misc-scripts/xref_mapping/XrefParser/MGDParser.pm
index c5bb48cb42..85b9aa5dc9 100644
--- a/misc-scripts/xref_mapping/XrefParser/MGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MGDParser.pm
@@ -4,11 +4,8 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
+use base qw( XrefParser::BaseParser );
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
-
my $xref_sth ;
my $dep_sth;
@@ -51,11 +48,14 @@ sub run {
my $mismatch = 0;
my %mgi_good;
- if(!open(FILE,"<". $file)){
- print "ERROR: Could not open file $file";
- return 1; # 1 is an error
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
+ print "ERROR: Could not open file $file";
+ return 1; # 1 is an error
}
- while(my $line = <FILE>){
+
+ while ( my $line = $file_io->getline() ) {
chomp $line;
my ($key,$label,$desc,$sps) = (split("\t",$line))[0,1,3,6];
my @sp = split(/\s/,$sps);
@@ -70,19 +70,21 @@ sub run {
}
}
}
- close FILE;
-
+ $file_io->close();
my $dir = dirname($file);
my $syn_file = $dir."/MRK_Synonym.sql.rpt";
- if(!open(FILE2,"<". $syn_file)){
- print "ERROR: Could not open file $syn_file";
+ $file_io = $self->get_filehandle($syn_file);
+
+ if ( !defined $file_io ) {
+ print "ERROR: Could not open file $syn_file";
return 1;
}
+
my $synonyms=0;
- while(<FILE2>){
+ while ( $_ = $file_io->getline() ) {
if(/MGI:/){
chomp ;
my ($key,$syn) = (split)[0,4];
@@ -92,23 +94,15 @@ sub run {
}
}
}
- close FILE2;
+
+ $file_io->close();
+
print "\t$count xrefs succesfully loaded\n";
print "\t$synonyms synonyms successfully loaded\n";
print "\t$mismatch xrefs failed to load\n";
return 0;
-
-
-}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::MGDParser";
- return $self;
-
}
-
+
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
index a21828179f..c634c09925 100644
--- a/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/MIMParser.pm
@@ -4,11 +4,7 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
-
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -52,16 +48,21 @@ sub run {
local $/ = "*RECORD*";
- if(!open(MIM,"<".$file)){
- print "ERROR: Could not open $file\n";
- return 1; # 1 is an error
+ my $mim_io = $self->get_filehandle($file);
+
+ if ( !defined $mim_io ) {
+ print "ERROR: Could not open $file\n";
+ return 1; # 1 is an error
}
-
+
my $gene = 0;
my $phenotype = 0;
my $removed_count =0;
- <MIM>; # first record is empty with *RECORD* as the record seperator
- while (<MIM>) {
+
+ $mim_io->getline(); # first record is empty with *RECORD* as the
+ # record seperator
+
+ while ( $_ = $mim_io->getline() ) {
#get the MIM number
my $number = 0;
my $description = undef;
@@ -101,6 +102,9 @@ sub run {
}
}
}
+
+ $mim_io->close();
+
my $syn_count =0;
foreach my $mim (keys %old_to_new){
my $old= $mim;
@@ -118,14 +122,4 @@ sub run {
return 0; #successful
}
-
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::MIMParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
index 7d188c3a6a..a56b154227 100644
--- a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
@@ -4,10 +4,7 @@ use strict;
use DBI;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Parse file of Ensembl - Vega OTTT transcript mappings
# ENST00000373795: OTTHUMT00000010392
@@ -19,17 +16,19 @@ sub run {
my ($self, $file, $source_id, $species_id) = @_;
- if(!open(OTTT,"<".$file)){
+ my $ottt_io = $self->get_filehandle($file);
+
+ if ( !defined $ottt_io ) {
print "Could not open $file\n";
return 1;
}
+
my $line_count = 0;
my $xref_count = 0;
my $xref_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$source_id AND species_id=$species_id");
- while (<OTTT>) {
-
+ while ( $_ = $ottt_io->getline() ) {
my ($ens, $ottt) = split;
$ens =~ s/://g;
@@ -48,19 +47,12 @@ sub run {
}
- print "Parsed $line_count OTTT identifiers from $file, added $xref_count xrefs and $line_count direct_xrefs\n";
+ $ottt_io->close();
- close(OTTT);
- return 0;
-}
-
-
-sub new {
+ print "Parsed $line_count OTTT identifiers from $file, added $xref_count xrefs and $line_count direct_xrefs\n";
- my $self = {};
- bless $self, "XrefParser::OTTTParser";
- return $self;
+ return 0;
}
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
index 6eb169a375..8f147c02a8 100644
--- a/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RGDParser.pm
@@ -4,10 +4,7 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
my $xref_sth ;
my $dep_sth;
@@ -47,11 +44,14 @@ sub run {
my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
- if(!open(RGD,"<".$file)){
+ my $rgd_io = $self->get_filehandle($file);
+
+ if ( !defined $rgd_io ) {
print "ERROR: Could not open $file\n";
return 1;
}
- my $line = <RGD>;
+
+ my $line = $rgd_io->getline();
chomp $line;
my @linearr = split(/\t/,$line);
@@ -74,7 +74,7 @@ sub run {
my $count= 0;
my $mismatch = 0;
- while ($line = <RGD>) {
+ while ( $line = $rgd_io->getline() ) {
chomp $line;
my ($rgd, $symbol, $name, $refseq) = (split (/\t/,$line))[0,1,2,16];
my @nucs = split(/\,/,$refseq);
@@ -94,6 +94,7 @@ sub run {
}
}
}
+
if(!$done){
# print STDERR "$rgd FAILED for $failed_list\n";
$self->add_xref("RGD:".$rgd,"",$symbol,$name,$source_id,$species_id);
@@ -101,18 +102,12 @@ sub run {
}
}
+
+ $rgd_io->close();
+
print "\t$count xrefs succesfully loaded and dependent on refseq\n";
print "\t$mismatch xrefs added but with NO dependencies\n";
return 0;
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::RGDParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
index 9a1392014f..efad047380 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm
@@ -6,10 +6,7 @@ use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw( XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -49,8 +46,10 @@ sub run {
my $pred_dna_source_id = XrefParser::BaseParser->get_source_id_for_source_name('RefSeq_dna_predicted');
print "RefSeq_peptide_predicted source ID = $pred_peptide_source_id; RefSeq_dna_predicted source ID = $pred_dna_source_id\n";
+ my $xrefs =
+ $self->create_xrefs( $peptide_source_id, $dna_source_id,
+ $pred_peptide_source_id, $pred_dna_source_id, $file, $species_id );
- my $xrefs = create_xrefs($peptide_source_id, $dna_source_id, $pred_peptide_source_id, $pred_dna_source_id, $file, $species_id);
if(!defined($xrefs)){
return 1; #error
}
@@ -68,8 +67,10 @@ sub run {
# Slightly different formats
sub create_xrefs {
+ my $self = shift;
- my ($peptide_source_id, $dna_source_id, $pred_peptide_source_id, $pred_dna_source_id, $file, $species_id) = @_;
+ my ( $peptide_source_id, $dna_source_id, $pred_peptide_source_id,
+ $pred_dna_source_id, $file, $species_id ) = @_;
my %name2species_id = XrefParser::BaseParser->name2species_id();
@@ -78,10 +79,13 @@ sub create_xrefs {
# my (%genemap) = %{XrefParser::BaseParser->get_valid_codes("mim_gene",$species_id)};
# my (%morbidmap) = %{XrefParser::BaseParser->get_valid_codes("mim_morbid",$species_id)};
- if(!open(REFSEQ, $file)){
+ my $refseq_io = $self->get_filehandle($file);
+
+ if ( !defined $refseq_io ) {
print "ERROR: Can't open RefSeqGPFF file $file\n";
return undef;
}
+
my @xrefs;
local $/ = "\/\/\n";
@@ -109,7 +113,7 @@ sub create_xrefs {
}
- while (<REFSEQ>) {
+ while ( $_ = $refseq_io->getline() ) {
my $xref;
@@ -224,7 +228,7 @@ sub create_xrefs {
} # while <REFSEQ>
- close (REFSEQ);
+ $refseq_io->close();
print "Read " . scalar(@xrefs) ." xrefs from $file\n";
@@ -234,14 +238,4 @@ sub create_xrefs {
# --------------------------------------------------------------------------------
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::RefSeqGPFFParser";
- return $self;
-
-}
-
-# --------------------------------------------------------------------------------
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
index 1557f53fc5..1625701a10 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm
@@ -6,10 +6,7 @@ use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -46,7 +43,10 @@ sub run {
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
}
- my $xrefs = create_xrefs($peptide_source_id, $dna_source_id, $pred_peptide_source_id, $pred_dna_source_id, $file, $species_id);
+ my $xrefs =
+ $self->create_xrefs( $peptide_source_id, $dna_source_id,
+ $pred_peptide_source_id, $pred_dna_source_id, $file, $species_id );
+
if(!defined($xrefs)){
return 1; #error
}
@@ -65,21 +65,25 @@ sub run {
# Slightly different formats
sub create_xrefs {
+ my $self = shift;
- my ($peptide_source_id, $dna_source_id, $pred_peptide_source_id, $pred_dna_source_id, $file, $species_id) = @_;
+ my ( $peptide_source_id, $dna_source_id, $pred_peptide_source_id,
+ $pred_dna_source_id, $file, $species_id ) = @_;
my %name2species_id = XrefParser::BaseParser->name2species_id();
- if(!open(REFSEQ, $file)){
- print "ERROR: Can't open RefSeq file $file\n";
- return undef;
+ my $refseq_io = $self->get_filehandle($file);
+
+ if ( !defined $refseq_io ) {
+ print "ERROR: Can't open RefSeq file $file\n";
+ return undef;
}
+
my @xrefs;
local $/ = "\n>";
- while (<REFSEQ>) {
-
+ while ( $_ = $refseq_io->getline() ) {
my $xref;
my $entry = $_;
@@ -92,7 +96,7 @@ sub create_xrefs {
(my $gi, my $n, my $ref, my $acc, my $description) = split(/\|/, $header);
my ($species, $mrna);
- if ($file =~ /\.faa$/) {
+ if ($file =~ /\.faa(\.gz|\.Z)?$/) {
($mrna, $description, $species) = $description =~ /(\S*)\s+(.*)\s+\[(.*)\]$/;
$xref->{SEQUENCE_TYPE} = 'peptide';
@@ -105,7 +109,7 @@ sub create_xrefs {
}
$xref->{SOURCE_ID} = $source_id;
- } elsif ($file =~ /\.fna$/) {
+ } elsif ($file =~ /\.fna(\.gz|\.Z)?$/) {
($species, $description) = $description =~ /\s*(\w+\s+\w+)\s+(.*)$/;
$xref->{SEQUENCE_TYPE} = 'dna';
@@ -126,8 +130,10 @@ sub create_xrefs {
my $species_id_check = $name2species_id{$species};
# skip xrefs for species that aren't in the species table
- if (defined($species_id) and $species_id == $species_id_check) {
-
+ if ( defined $species_id
+ && defined $species_id_check
+ && $species_id == $species_id_check )
+ {
my ($acc_no_ver,$ver) = split (/\./,$acc);
$xref->{ACCESSION} = $acc_no_ver;
$xref->{VERSION} = $ver;
@@ -144,7 +150,7 @@ sub create_xrefs {
}
- close (REFSEQ);
+ $refseq_io->close();
print "Read " . scalar(@xrefs) ." xrefs from $file\n";
@@ -154,14 +160,4 @@ sub create_xrefs {
# --------------------------------------------------------------------------------
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::RefSeqParser";
- return $self;
-
-}
-
-# --------------------------------------------------------------------------------
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
index e1dcec0067..96a376aae4 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm
@@ -4,10 +4,7 @@ use strict;
use DBI;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Parse file of Refseq records and assign direct xrefs
@@ -15,13 +12,13 @@ sub run {
my ($self, $file, $source_id, $species_id) = @_;
- if(!open(REFSEQ,"<".$file)){
+ my $refseq_io = $self->get_filehandle($file);
+
+ if ( defined $refseq_io ) {
print "Could not open $file\n";
return 1;
}
-
-
# becouse the direct mapping have no descriptions etc
# we have to steal these from the previous Refseq parser.
@@ -67,8 +64,10 @@ sub run {
my $xref_count = 0;
my %seen;
my %old_to_new;
- <REFSEQ>; # header
- while(<REFSEQ>){
+
+ $refseq_io->getline(); # header
+
+ while ( $_ = $refseq_io->getline() ) {
chomp;
my ($ccds,$refseq) = split;
@@ -102,19 +101,12 @@ sub run {
}
}
- print "Parsed $line_count RefSeq_dna identifiers from $file, added $xref_count xrefs and $xref_count direct_xrefs from $line_count lines.\n";
-
- close(REFSEQ);
- return 0;
-
-}
+ $refseq_io->close();
+ print "Parsed $line_count RefSeq_dna identifiers from $file, added $xref_count xrefs and $xref_count direct_xrefs from $line_count lines.\n";
-sub new {
- my $self = {};
- bless $self, "XrefParser::RefSeq_CCDSParser";
- return $self;
+ return 0;
}
diff --git a/misc-scripts/xref_mapping/XrefParser/SGDParser.pm b/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
index d6beb15afd..8d1f89f604 100644
--- a/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/SGDParser.pm
@@ -4,11 +4,7 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
-
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -40,15 +36,17 @@ sub run {
- if(!open(SGD,"<".$file)){
- print "ERROR: Could not open $file\n";
- return 1; # 1 is an error
+ my $sgd_io = $self->get_filehandle($file);
+
+ if ( !defined $sgd_io ) {
+ print "ERROR: Could not open $file\n";
+ return 1; # 1 is an error
}
my $xref_count =0;
my $syn_count =0;
- while (<SGD>) {
+ while ( $_ = $sgd_io->getline() ) {
chomp;
my ($locus_name, $alias_name, $desc, $gene_prod, $phenotype, $orf_name, $sgd_id) = split(/\t/,$_);
@@ -60,18 +58,11 @@ sub run {
$syn_count++;
}
}
+
+ $sgd_io->close();
+
print $xref_count." SGD Xrefs added with $syn_count synonyms\n";
return 0; #successful
}
-
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::SGDParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm b/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
index 8d5605cb3b..8ff59a44db 100644
--- a/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/SegmentParser.pm
@@ -4,10 +4,7 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -41,11 +38,14 @@ sub run {
my %name_2_source_id=();
my $added=0;
- if(!open(FILE,"<". $file)){
- print "ERROR: Could not open file $file\n";
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
+ print "ERROR: Could not open file $file\n";
return 1;
}
- while(my $line = <FILE>){
+
+ while ( my $line = $file_io->getline() ) {
chomp $line;
my ($gene_id,$transcript_id,$source_name,$acc,$display_label,$description, $status)
= split("\t",$line);
@@ -68,19 +68,11 @@ sub run {
#the those mapped to the transcript to the genes anyway due to the
#biomart check
}
- close FILE;
+
+ $file_io->close();
print "Added $added Xrefs for Gene segments\n";
return 0;
}
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::SegmentParser";
- return $self;
-
-}
-
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm b/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm
index 1d6f7e1faf..fd0680d935 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm
@@ -6,10 +6,7 @@ use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -41,7 +38,11 @@ sub run {
if(!defined($species_id)){
$species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
}
-my $xrefs =create_xrefs($unigene_source_id, $unigene_source_id, $file, $species_id);
+
+ my $xrefs =
+ $self->create_xrefs( $unigene_source_id, $unigene_source_id, $file,
+ $species_id );
+
if(!defined($xrefs)){
return 1; #error
}
@@ -56,23 +57,24 @@ my $xrefs =create_xrefs($unigene_source_id, $unigene_source_id, $file, $species_
my %geneid_2_desc;
sub get_desc{
+ my $self = shift;
my $file = shift;
+
my $dir = dirname($file);
-
(my $name) = $file =~ /\/(\w+)\.seq\.uniq/;
print $name."\n";
local $/ = "//";
+ my $desc_io = $self->get_filehandle( $dir . '/' . $name . '.data' );
- if(!open (DESC, "$dir/$name.data")){
+ if ( !defined $desc_io ) {
print "ERROR: Can't open $dir/$name.data\n";
return undef;
}
- while(<DESC>){
-
+ while ( $_ = $desc_io->getline() ) {
#ID Hs.159356
#TITLE Hypothetical LOC388277
@@ -82,21 +84,27 @@ sub get_desc{
$geneid_2_desc{$id} = $descrip;
}
+
+ $desc_io->close();
+
return 1;
}
sub create_xrefs {
+ my $self = shift;
- my ($peptide_source_id, $unigene_source_id, $file, $species_id) = @_;
+ my ( $peptide_source_id, $unigene_source_id, $file, $species_id ) = @_;
my %name2species_id = XrefParser::BaseParser->name2species_id();
- if(!defined(get_desc($file))){
+ if ( !defined( $self->get_desc($file) ) ) {
return undef;
}
- if(!open(UNIGENE, $file)){
+ my $unigene_io = $self->get_filehandle($file);
+
+ if ( !defined $unigene_io ) {
print "Can't open RefSeq file $file\n";
return undef;
}
@@ -110,7 +118,7 @@ sub create_xrefs {
local $/ = "\n>";
- while (<UNIGENE>) {
+ while ( $_ = $unigene_io->getline() ) {
my $xref;
@@ -150,7 +158,8 @@ sub create_xrefs {
}
- close (UNIGENE);
+ $unigene_io->close();
+
%geneid_2_desc=();
print "Read " . scalar(@xrefs) ." xrefs from $file\n";
@@ -158,16 +167,4 @@ sub create_xrefs {
}
-# --------------------------------------------------------------------------------
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::UniGeneParser";
- return $self;
-
-}
-
-# --------------------------------------------------------------------------------
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
index 97c5dcdf03..e15ad5a66a 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtParser.pm
@@ -13,10 +13,7 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -54,7 +51,10 @@ sub run {
print "SpTREMBL source id for $file: $sptr_source_id\n";
- my @xrefs = create_xrefs($sp_source_id, $sptr_source_id, $species_id, $file);
+ my @xrefs =
+ $self->create_xrefs( $sp_source_id, $sptr_source_id, $species_id,
+ $file );
+
if ( !@xrefs ) {
return 1; # 1 error
}
@@ -110,8 +110,9 @@ sub get_species {
# Parse file into array of xref objects
sub create_xrefs {
+ my $self = shift;
- my ($sp_source_id, $sptr_source_id, $species_id, $file) = @_;
+ my ( $sp_source_id, $sptr_source_id, $species_id, $file ) = @_;
my $num_sp = 0;
my $num_sptr = 0;
@@ -135,15 +136,14 @@ sub create_xrefs {
my (%genemap) = %{XrefParser::BaseParser->get_valid_codes("mim_gene",$species_id)};
my (%morbidmap) = %{XrefParser::BaseParser->get_valid_codes("mim_morbid",$species_id)};
- if(!open(UNIPROT, $file)){
- print"Can't open Swissprot file $file\n";
- return undef;
- }
+ my $uniprot_io = $self->get_filehandle($file);
+ if ( !defined $uniprot_io ) { return undef }
+
my @xrefs;
- local $/ = "\/\/\n";
+ local $/ = "//\n";
- while (<UNIPROT>) {
+ while ( $_ = $uniprot_io->getline() ) {
# if an OX line exists, only store the xref if the taxonomy ID that the OX
# line refers to is in the species table
@@ -353,7 +353,7 @@ sub create_xrefs {
}
- close (UNIPROT);
+ $uniprot_io->close();
print "Read $num_sp SwissProt xrefs and $num_sptr SPTrEMBL xrefs from $file\n";
print "Found $num_sp_pred predicted SwissProt xrefs and $num_sptr_pred predicted SPTrEMBL xrefs\n" if ($num_sp_pred > 0 || $num_sptr_pred > 0);
@@ -363,16 +363,4 @@ sub create_xrefs {
#TODO - currently include records from other species - filter on OX line??
}
-# --------------------------------------------------------------------------------
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::UniProtParser";
- return $self;
-
-}
-
-# --------------------------------------------------------------------------------
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm b/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm
index 0486f04a67..9001395c49 100644
--- a/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm
@@ -5,10 +5,7 @@ package XrefParser::UniProtVarSplicParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# UniProtVarSplic file format: fasta, e.g.
@@ -27,17 +24,18 @@ sub run {
local $/ = "\n>";
- if(!open(FILE,"<".$file)){
- print "ERROR: Could not open $file\n";
- return 1; # 1 error
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
+ print "ERROR: Could not open $file\n";
+ return 1; # 1 error
}
my $species_tax_id = $self->get_taxonomy_from_species_id($species_id);
my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
my $missed = 0;
- while (<FILE>) {
-
+ while ( $_ = $file_io->getline() ) {
my $xref;
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
@@ -69,7 +67,7 @@ sub run {
}
}
- close (FILE);
+ $file_io->close();
print $missed." ignored as original uniprot not found in database\n";
print scalar(@xrefs) . " UniProtVarSplic xrefs succesfully parsed\n";
@@ -80,15 +78,4 @@ sub run {
return 0;
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::UniProtVarSplicParser";
- return $self;
-
-}
-
1;
-
-
diff --git a/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm b/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
index fcd0eda3da..df059b421c 100644
--- a/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm
@@ -2,16 +2,12 @@ package XrefParser::WilsonAffyParser;
use strict;
-use XrefParser::BaseParser;
+use base qw( XrefParser::BaseParser );
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
my $xref_sth ;
my $dep_sth;
my $syn_sth;
-
-
sub run {
my ($self, $file, $source_id, $species_id) = @_;
@@ -39,14 +35,16 @@ sub create_xrefs {
my @xrefs;
- if(!open(FILE,"<".$file)){
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
print "ERROR: Could not open $file\n";
- return 1; # 1 error
+ return 1; # 1 error
}
- <FILE>; # skip first line
- while (<FILE>) {
+ $file_io->getline(); # skip first line
+ while ( $_ = $file_io->getline() ) {
#last if ($count > 200);
my $xref;
@@ -79,10 +77,13 @@ sub create_xrefs {
# fetch sequence for others (EMBL ESTs and RefSeqs - pfetch will handle these)
system ("pfetch -q $target > seq.txt");
- open(SEQ, "<seq.txt");
- my $seq = <SEQ>;
+
+ my $seq_io = $self->get_filehandle('seq.txt');
+
+ my $seq = $seq_io->getline();
+ $seq_io->close();
+
chomp($seq);
- close(SEQ);
if ($seq && $seq !~ /no match/) {
@@ -116,7 +117,7 @@ sub create_xrefs {
}
- close(FILE);
+ $file_io->close();
print "\n\nParsed $count primary xrefs.\n";
print "Couldn't get sequence for $noseq primary_xrefs\n" if ($noseq);
@@ -126,12 +127,4 @@ sub create_xrefs {
}
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::WilsonAffyParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
index c31253be7d..8f27dbfb86 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormPepParser.pm
@@ -3,10 +3,8 @@ package XrefParser::WormPepParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
+use base qw( XrefParser::BaseParser );
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
my $xref_sth ;
my $dep_sth;
@@ -31,15 +29,17 @@ sub run {
my $xref_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$worm_source_id AND species_id=$species_id");
my $xref_sth2 = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$worm_locus_id AND species_id=$species_id");
- if(!open(PEP,"<".$file)){
+ my $pep_io = $self->get_filehandle($file);
+
+ if ( !defined $pep_io ) {
print "ERROR: Could not open $file\n";
- return 1; # 1 error
+ return 1; # 1 error
}
- my ($x_count, $d_count);
+ my ($x_count, $d_count);
- while (<PEP>) {
+ while ( $_ = $pep_io->getline() ) {
my ($transcript, $wb, $display) = (split(/\t/,substr($_,1)))[0,1,2];
# reuse or create xref
@@ -69,19 +69,10 @@ sub run {
$d_count++;
}
- close (PEP);
+ $pep_io->close();
print "Added $d_count direct xrefs and $x_count xrefs\n";
return 0;
}
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::WormPepParser";
- return $self;
-
-}
-
1;
-
diff --git a/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm b/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm
index c18fa62366..92d43cabed 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm
@@ -7,10 +7,7 @@ package XrefParser::WormbaseDatabaseStableIDParser;
use strict;
-use XrefParser::DatabaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::DatabaseParser);
+use base qw( XrefParser::DatabaseParser );
sub run {
@@ -46,13 +43,5 @@ sub run {
return 0;
}
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::WormbaseDatabaseStableIDParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm b/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm
index 452855aea8..02c1e7591f 100644
--- a/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm
@@ -5,10 +5,7 @@ package XrefParser::XenopusJamboreeParser;
use strict;
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# Xenopus Jamboree peptides file format: fasta, e.g.
@@ -24,14 +21,16 @@ sub run {
local $/ = "\n>";
- if(!open(FILE,"<".$file)){
+ my $file_io = $self->getline($file);
+
+ if ( !defined $file_io ) {
print "ERROR: Could not open $file\n";
- return 1; # 1 error
+ return 1; # 1 error
}
- my $species_tax_id = $self->get_taxonomy_from_species_id($species_id);
- while (<FILE>) {
+ my $species_tax_id = $self->get_taxonomy_from_species_id($species_id);
+ while ( $_ = $file_io->getline() ) {
my $xref;
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
@@ -57,7 +56,7 @@ sub run {
}
- close (FILE);
+ $file_io->close();
print scalar(@xrefs) . " XenopusJamboreeParser xrefs succesfully parsed\n";
@@ -69,13 +68,4 @@ sub run {
return 0;
}
-
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::XenopusJamboreeParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm b/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
index 4875998fe4..83ceda1bcf 100644
--- a/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ZFINParser.pm
@@ -4,12 +4,7 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
-
-
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -45,10 +40,13 @@ sub run {
my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
- if(!open(SWISSPROT,"<".$dir."/swissprot.txt")){
- print "ERROR: Could not open $dir/swissprot.txt\n";
- return 1; # 1 error
+ my $swissprot_io = $self->get_filehandle( $dir . '/swissprot.txt' );
+
+ if ( !defined $swissprot_io ) {
+ print "ERROR: Could not open $dir/swissprot.txt\n";
+ return 1; # 1 error
}
+
#e.g.
#ZDB-GENE-000112-30 couptf2 O42532
#ZDB-GENE-000112-32 couptf3 O42533
@@ -58,7 +56,8 @@ sub run {
my $spcount =0;
my $rscount =0;
my $mismatch=0;
- while (<SWISSPROT>) {
+
+ while ( $_ = $swissprot_io->getline() ) {
chomp;
my ($zfin, $label, $acc) = split (/\s+/,$_);
if(defined($swiss{$acc})){
@@ -69,16 +68,21 @@ sub run {
$mismatch++;
}
}
- close SWISSPROT;
-
- if(!open(REFSEQ,"<".$dir."/refseq.txt")){
- print "ERROR: Could not open $dir/refseq.txt\n";
+
+ $swissprot_io->close();
+
+ my $refseq_io = $self->get_filehandle( $dir . '/refseq.txt' );
+
+ if ( !defined $refseq_io ) {
+ print "ERROR: Could not open $dir/refseq.txt\n";
return 1;
}
+
#ZDB-GENE-000125-12 igfbp2 NM_131458
#ZDB-GENE-000125-12 igfbp2 NP_571533
#ZDB-GENE-000125-4 dlc NP_571019
- while (<REFSEQ>) {
+
+ while ( $_ = $refseq_io->getline() ) {
chomp;
my ($zfin, $label, $acc) = split (/\s+/,$_);
if(defined($refseq{$acc})){
@@ -89,18 +93,12 @@ sub run {
$mismatch++;
}
}
- close REFSEQ;
+
+ $refseq_io->close();
+
print "\t$spcount xrefs from Swissprot and $rscount xrefs from RefSeq succesfully loaded\n";
print "\t$mismatch xrefs ignored\n";
return 0;
}
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::ZFINParser";
- return $self;
-
-}
-
1;
diff --git a/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm b/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
index 92710ba9cc..8ca57774fb 100644
--- a/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm
@@ -4,10 +4,7 @@ use strict;
use POSIX qw(strftime);
use File::Basename;
-use XrefParser::BaseParser;
-
-use vars qw(@ISA);
-@ISA = qw(XrefParser::BaseParser);
+use base qw( XrefParser::BaseParser );
# --------------------------------------------------------------------------------
# Parse command line and run if being run directly
@@ -41,11 +38,14 @@ sub run {
my %name_2_source_id=();
my $added=0;
- if(!open(FILE,"<". $file)){
- print "ERROR: Could not open file $file\n";
+ my $file_io = $self->get_filehandle($file);
+
+ if ( !defined $file_io ) {
+ print "ERROR: Could not open file $file\n";
return 1;
}
- while(my $line = <FILE>){
+
+ while ( my $line = $file_io->getline() ) {
chomp $line;
my ($gene_id,$transcript_id,$source_name,$acc,$display_label,$full_description, $status)
= split("\t",$line);
@@ -79,19 +79,11 @@ sub run {
#biomart check
# $self->add_direct_xref($xref_id, $gene_id, "Gene", "") if (defined($gene_id));
}
- close FILE;
+
+ $file_io->close();
print "Added $added Xrefs for ncRNAs\n";
return 0;
}
-sub new {
-
- my $self = {};
- bless $self, "XrefParser::ncRNAParser";
- return $self;
-
-}
-
-
1;
diff --git a/misc-scripts/xref_mapping/xref_parser.pl b/misc-scripts/xref_mapping/xref_parser.pl
index 5d401928e1..2fe667106f 100644
--- a/misc-scripts/xref_mapping/xref_parser.pl
+++ b/misc-scripts/xref_mapping/xref_parser.pl
@@ -3,36 +3,45 @@ use strict;
use Getopt::Long;
use XrefParser::BaseParser;
-my ($host, $port, $dbname, $user, $pass, @species, @sources, $skipdownload, $checkdownload, $create, $release, $cleanup, $drop_existing_db, $deletedownloaded, $dl_path, @notsource);
-
-GetOptions('dbuser|user=s' => \$user,
- 'dbpass|pass=s' => \$pass,
- 'dbhost|host=s' => \$host,
- 'dbport|port=i' => \$port,
- 'dbname=s' => \$dbname,
- 'species=s' => \@species,
- 'source=s' => \@sources,
- 'download_dir=s' => \$dl_path,
- 'skipdownload' => \$skipdownload, # skips all downloads
- 'checkdownload!' => \$checkdownload, # if file exists it won't be downloaded
- 'create' => \$create,
- 'setrelease=s' => \$release,
- 'cleanup' => \$cleanup,
- 'notsource=s' => \@notsource,
- 'drop_db|dropdb!' => \$drop_existing_db, # drops xref db without user interaction
- 'delete_downloaded' => \$deletedownloaded,
- 'download_path=s' => \$dl_path,
- 'help' => sub { usage(); exit(0); });
+my (
+ $host, $port, $dbname,
+ $user, $pass, @species,
+ @sources, $skipdownload, $checkdownload,
+ $create, $release, $cleanup,
+ $drop_existing_db, $deletedownloaded, $dl_path,
+ @notsource, $compressed
+);
+
+GetOptions(
+ 'dbuser|user=s' => \$user,
+ 'dbpass|pass=s' => \$pass,
+ 'dbhost|host=s' => \$host,
+ 'dbport|port=i' => \$port,
+ 'dbname=s' => \$dbname,
+ 'species=s' => \@species,
+ 'source=s' => \@sources,
+ 'download_dir=s' => \$dl_path,
+ 'skipdownload' => \$skipdownload, # skips all downloads
+ 'checkdownload!' => \$checkdownload, # don't download if exists
+ 'create' => \$create,
+ 'setrelease=s' => \$release,
+ 'cleanup' => \$cleanup,
+ 'notsource=s' => \@notsource,
+ 'drop_db|dropdb!' =>
+ \$drop_existing_db, # drops xref db without user interaction
+ 'delete_downloaded' => \$deletedownloaded,
+ 'download_path=s' => \$dl_path,
+ 'compressed' => \$compressed, # don't force decompression of files
+ 'help' => sub { usage(); exit(0); }
+);
@species = split(/,/,join(',',@species));
@sources = split(/,/,join(',',@sources));
-if (!$user || !$host || !$dbname) {
-
- usage();
- exit(1);
-
+if ( !$user || !$host || !$dbname ) {
+ usage();
+ exit(1);
}
XrefParser::BaseParser::run(
@@ -43,7 +52,8 @@ XrefParser::BaseParser::run(
$checkdownload, $create,
$release, $cleanup,
$drop_existing_db, $deletedownloaded,
- $dl_path, \@notsource
+ $dl_path, \@notsource,
+ $compressed
);
# --------------------------------------------------------------------------------
--
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